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#编者信息
熊荣川
明湖实验室
xiongrongchuan@126.com
http://blog.sciencenet.cn/u/Bearjazz
Ancestral state reconstruction : Continuous characters can be reconstructed using maximum likelihood, generalised least squares or independent contrasts in ape. Root ancestral character states under Brownian motion or Ornstein-Uhlenbeck models can be reconstructed in ouch, though ancestral states at the internal nodes are not. Discrete characters can be reconstructed using a variety of Markovian models that parameterize the transition rates among states using ape. markophylo can fit a broad set of discrete character types with models that can incorporate constrained substitution rates, rate partitioning across sites, branch-specific rates, sampling bias, and non-stationary root probabilities. phytools can do stochastic character mapping of traits on trees.
| 祖先状态重建:连续性特征可以使用apee包中最大似然法、一般最小二乘法或独立对比方法重建。在ouch中可用Brownian motion或Ornstein-Uhlenbeck模型,确定根部祖先特征状态,而内部节点的祖先状态则不能。使用ape将状态之间的转换率参数化后,离散特征可以使用各种马尔可夫模型重建。markophylo可以适配广泛的离散特征类型,设定约束替换率、跨位点的速率分配、特定分支速率、采样偏差和非静态根概率的模型。phytools可以在树上进行随机特征标注。 |
https://cran.r-project.org/web/views/Phylogenetics.html |
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